A scene soon to be in Simpsons Fantasy VIII (though Lisa will be older in the game then she is in this pic, in fact, she'll be 24)

It seems that Dark Maggie is starting to manipulate time for her own use. Hearing what happened about Virgil, she goes back to 1860 and helps Colonel Burns prevent Virgil from escaping with Mabel. In the year 2016, Lisa, Maggie and Lucy find out and go back to set things right. While Lisa holds off Colonel Burns alone with Eliza, Maggie and Lucy aid Mabel and Virgil's escape.

Don't forget that by helping Virgil to escape to Canada, Mabel would've been branded a wanted criminal, something she might not have wanted her daughter to live through, so she may have left Eliza with Hiram for that reason.